266 lines
10 KiB
MySQL
266 lines
10 KiB
MySQL
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-- ------------------------------------------------------------------
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-- Mortality verification for Sepsis-3 in MIMIC-III v1.3.
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--
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-- Usage:
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-- psql -d mimic -v ON_ERROR_STOP=1 \
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-- -c 'SET search_path TO mimiciii, public;' \
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-- -f sql/sepsis/mortality_checks.sql
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--
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-- Purpose:
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-- `sanity_checks.sql` reported a 14.6% in-hospital mortality among
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-- Sepsis-3 = TRUE patients, well below the 25-35% range in the
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-- literature. The hypothesis was that the broad cohort (neonates,
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-- re-admissions, short stays included) drags the number down.
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--
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-- This script walks an exclusion funnel and shows mortality at
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-- each step so you can confirm. It also shows 30-day mortality,
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-- stratification by age band, and a direct comparison with the
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-- numbers published in:
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--
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-- Johnson AEW et al., Crit Care Med 2018.
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-- "A Comparative Analysis of Sepsis Identification Methods
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-- in an Electronic Database."
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-- Reported on MIMIC-III v1.4 with adult, first-ICU-stay,
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-- LOS >= 4 h cohort:
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-- n = 21 927 sepsis-3 stays
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-- in-hospital mortality = 21.0%
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-- 30-day mortality = 25.4%
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--
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-- All ages use a clamp at 91 (MIMIC-III shifts DOB by 300 y for
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-- patients > 89; we treat them as 91 for stratification).
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-- ------------------------------------------------------------------
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\set ON_ERROR_STOP on
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\timing on
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-- Build a working cohort table once with everything we need
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DROP TABLE IF EXISTS sepsis3_cohort_check;
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CREATE TEMP TABLE sepsis3_cohort_check AS
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SELECT ie.subject_id
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, ie.hadm_id
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, ie.icustay_id
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, ie.intime
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, ie.outtime
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, ie.first_careunit
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, EXTRACT(EPOCH FROM (ie.outtime - ie.intime)) / 3600.0 AS los_hours
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, LEAST(
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91.0,
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EXTRACT(EPOCH FROM (ie.intime - pat.dob))
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/ (365.242 * 86400.0)
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) AS age_at_intime
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, ROW_NUMBER() OVER (
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PARTITION BY ie.subject_id
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ORDER BY ie.intime
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) AS icustay_seq
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, adm.hospital_expire_flag AS died_in_hospital
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, (pat.dod IS NOT NULL
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AND pat.dod <= ie.intime + INTERVAL '30 days')::int AS died_within_30d
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, COALESCE(s.sepsis3, FALSE) AS sepsis3
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FROM icustays ie
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JOIN admissions adm ON adm.hadm_id = ie.hadm_id
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JOIN patients pat ON pat.subject_id = ie.subject_id
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LEFT JOIN sepsis3 s ON s.icustay_id = ie.icustay_id;
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CREATE INDEX ON sepsis3_cohort_check (icustay_id);
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ANALYZE sepsis3_cohort_check;
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\echo
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\echo '=================================================================='
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\echo ' 1. Cohort exclusion funnel (incremental filtering)'
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\echo '=================================================================='
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\echo "Each row applies an additional restriction. The 'sepsis3' columns"
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\echo "report stats among rows where sepsis3 = TRUE within that cohort."
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\echo
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\echo "EXPECTED progression: as we narrow to the canonical adult/first-stay/"
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\echo "LOS >= 24h cohort, in-hospital mortality among Sepsis-3 should rise"
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\echo "from ~14% toward ~25-30%."
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\echo
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WITH levels AS (
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-- 0. Everyone
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SELECT 0 AS lvl, '0. all icustays' AS step
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, c.* FROM sepsis3_cohort_check c
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UNION ALL
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-- 1. Exclude neonatal ICU
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SELECT 1, '1. + exclude NICU'
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, c.* FROM sepsis3_cohort_check c
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WHERE c.first_careunit != 'NICU'
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UNION ALL
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-- 2. Adult (age >= 18) on top of (1)
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SELECT 2, '2. + age >= 18'
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, c.* FROM sepsis3_cohort_check c
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WHERE c.first_careunit != 'NICU'
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AND c.age_at_intime >= 18
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UNION ALL
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-- 3. First ICU stay only on top of (2)
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SELECT 3, '3. + first ICU stay only'
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, c.* FROM sepsis3_cohort_check c
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WHERE c.first_careunit != 'NICU'
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AND c.age_at_intime >= 18
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AND c.icustay_seq = 1
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UNION ALL
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-- 4. LOS >= 24h on top of (3) -- the canonical Seymour cohort
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SELECT 4, '4. + LOS >= 24 h (canonical)'
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, c.* FROM sepsis3_cohort_check c
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WHERE c.first_careunit != 'NICU'
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AND c.age_at_intime >= 18
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AND c.icustay_seq = 1
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AND c.los_hours >= 24
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)
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SELECT lvl
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, step
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, count(*) AS n_total
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, sum(CASE WHEN sepsis3 THEN 1 ELSE 0 END) AS n_sepsis3
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, round(100.0 * sum(CASE WHEN sepsis3 THEN 1 ELSE 0 END)
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/ count(*), 1) AS pct_sepsis3
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-- in-hospital mortality among Sepsis-3 = TRUE
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, round(100.0 * sum(CASE WHEN sepsis3 AND died_in_hospital = 1
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THEN 1 ELSE 0 END)
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/ NULLIF(sum(CASE WHEN sepsis3 THEN 1 ELSE 0 END), 0), 1)
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AS sep_inhosp_pct
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-- 30-day mortality among Sepsis-3 = TRUE
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, round(100.0 * sum(CASE WHEN sepsis3 AND died_within_30d = 1
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THEN 1 ELSE 0 END)
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/ NULLIF(sum(CASE WHEN sepsis3 THEN 1 ELSE 0 END), 0), 1)
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AS sep_30d_pct
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-- in-hospital mortality among NOT Sepsis-3
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, round(100.0 * sum(CASE WHEN NOT sepsis3 AND died_in_hospital = 1
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THEN 1 ELSE 0 END)
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/ NULLIF(sum(CASE WHEN NOT sepsis3 THEN 1 ELSE 0 END), 0), 1)
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AS nonsep_inhosp_pct
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FROM levels
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GROUP BY lvl, step
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ORDER BY lvl;
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\echo
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\echo '=================================================================='
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\echo ' 2. Mortality stratified by age band, canonical cohort only'
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\echo '=================================================================='
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\echo "EXPECTED:"
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\echo " Mortality among Sepsis-3 = TRUE rises monotonically with age."
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\echo " Adults < 30: ~10-15%"
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\echo " 30 - 50: ~15-20%"
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\echo " 50 - 70: ~20-25%"
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\echo " 70 - 90+: ~30-40%"
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\echo
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SELECT CASE
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WHEN age_at_intime < 30 THEN '1. <30'
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WHEN age_at_intime < 50 THEN '2. 30-49'
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WHEN age_at_intime < 70 THEN '3. 50-69'
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WHEN age_at_intime < 90 THEN '4. 70-89'
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ELSE '5. 90+'
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END AS age_band
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, count(*) AS n_sepsis3
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, round(100.0 * sum(died_in_hospital) / count(*), 1) AS pct_inhosp
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, round(100.0 * sum(died_within_30d) / count(*), 1) AS pct_30d
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FROM sepsis3_cohort_check
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WHERE sepsis3
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AND first_careunit != 'NICU'
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AND age_at_intime >= 18
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AND icustay_seq = 1
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AND los_hours >= 24
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GROUP BY 1
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ORDER BY 1;
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\echo
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\echo '=================================================================='
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\echo ' 3. Mortality stratified by max-SOFA day-1 (canonical cohort)'
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\echo '=================================================================='
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\echo "EXPECTED:"
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\echo " Mortality should rise monotonically with SOFA. This is the"
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\echo " classic dose-response curve of organ dysfunction vs death,"
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\echo " and is the strongest semantic check that the SOFA pipeline"
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\echo " itself is computing the right thing."
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\echo " SOFA 0-3: ~5-10%"
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\echo " SOFA 4-7: ~15-25%"
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\echo " SOFA 8-11: ~30-40%"
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\echo " SOFA 12+: ~50-65%"
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\echo
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WITH d1 AS (
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SELECT icustay_id, max(sofa_24hours) AS d1_sofa
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FROM sofa_hourly
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WHERE hr <= 24
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GROUP BY icustay_id
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)
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SELECT CASE
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WHEN d1_sofa <= 3 THEN '1. 0-3'
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WHEN d1_sofa <= 7 THEN '2. 4-7'
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WHEN d1_sofa <= 11 THEN '3. 8-11'
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ELSE '4. 12+'
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END AS sofa_band
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, count(*) AS n
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, round(100.0 * sum(died_in_hospital) / count(*), 1) AS pct_inhosp
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, round(100.0 * sum(died_within_30d) / count(*), 1) AS pct_30d
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FROM sepsis3_cohort_check c
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JOIN d1 USING (icustay_id)
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WHERE first_careunit != 'NICU'
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AND age_at_intime >= 18
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AND icustay_seq = 1
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AND los_hours >= 24
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GROUP BY 1
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ORDER BY 1;
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\echo
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\echo '=================================================================='
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\echo ' 4. Direct comparison with Johnson 2018 (canonical cohort)'
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\echo '=================================================================='
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\echo "Johnson 2018 published numbers for Sepsis-3 on MIMIC-III v1.4"
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\echo "with the cohort: adult, first ICU stay only, LOS >= 4 h."
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\echo "They reported:"
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\echo " n_sepsis3 = 21 927"
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\echo " in-hospital pct_died = 21.0%"
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\echo " 30-day pct_died = 25.4%"
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\echo
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\echo "We use LOS >= 24 h here (the more common Seymour 2016 cutoff),"
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\echo "so our n will be a bit smaller and our mortality slightly"
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\echo "higher than Johnson's."
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\echo
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SELECT count(*) AS n_sepsis3
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, round(100.0 * sum(died_in_hospital) / count(*), 1) AS pct_inhosp
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, round(100.0 * sum(died_within_30d) / count(*), 1) AS pct_30d
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FROM sepsis3_cohort_check
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WHERE sepsis3
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AND first_careunit != 'NICU'
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AND age_at_intime >= 18
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AND icustay_seq = 1
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AND los_hours >= 24;
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\echo
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\echo '=================================================================='
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\echo ' 5. Sanity: where did the missing mortality "go"?'
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\echo '=================================================================='
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\echo "Decompose the gap between the broad-cohort 14.6% and the"
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\echo "canonical-cohort number from section 4. This shows how much"
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\echo "of the gap is explained by each filter individually."
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\echo
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WITH s3 AS (
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SELECT * FROM sepsis3_cohort_check WHERE sepsis3
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)
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SELECT 'all sepsis3' AS slice
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, count(*) AS n
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, round(100.0 * sum(died_in_hospital)/count(*), 1) AS pct_inhosp
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FROM s3
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UNION ALL SELECT 'NICU only',
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count(*), round(100.0 * sum(died_in_hospital)/count(*), 1)
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FROM s3 WHERE first_careunit = 'NICU'
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UNION ALL SELECT 'age < 18 only',
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count(*), round(100.0 * sum(died_in_hospital)/count(*), 1)
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FROM s3 WHERE age_at_intime < 18
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UNION ALL SELECT 're-admission only',
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count(*), round(100.0 * sum(died_in_hospital)/count(*), 1)
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FROM s3 WHERE icustay_seq > 1
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UNION ALL SELECT 'LOS < 24h only',
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count(*), round(100.0 * sum(died_in_hospital)/count(*), 1)
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FROM s3 WHERE los_hours < 24;
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\echo
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\echo 'Done. Compare the section-4 result to Johnson 2018 (~21% in-hospital,'
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\echo '~25% 30-day) for the headline check.'
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