Epidemiology of Adult Sepsis Events

Objective

• Identify adult sepsis events using the CDC Adult Sepsis Event Toolkit criteria using the Common Longitudinal Intensive Format (CLIF) 2.0 data structure.
• Determine the effect of including lactate in the definition on sepsis prevalence and mortality rates

Required CLIF tables and fields

Please refer to the online CLIF data dictionary, ETL tools, and specific table contacts for more information on constructing the required tables and fields. List all required tables for the project here, and provide a brief rationale for why they are required.

To identify hospitalizations and describe demographics:

• patient
• hospitalization
• ADT

To identify presumed infection

• microbiology_culture for blood culture collection
  • only blood culture collection data necessary, e.g. fluid_category = "Blood/Buffy Coat", collect_dttm, and component_category == "culture" required
• medication_admin_intermittent for qualifying antibiotic days
  • only med_group == "qualifying_CMS_antibiotics required (list of med_categories below)
  • med_route_name and med_route_category also required

To identify organ dysfunction

• labs
  • lab_category %in% c("lactate", "creatinine", "bilirubin_total", "platelet_count")
• vitals
• medication_admin_continuous
  • med_category %in% c("norepinephrine", "epinephrine", "phenylephrine", "vasopressin", "dopamine", "angiotensin")
• respiratory_support
  • only hospitalization_id, recorded_dttm, and device_category == "IMV" required

Cohort identification

Adults admitted to inpatient status (location_category %in% c("Ward", "ICU") from 1/1/2020 to 12/31/2021

start_date <- "2020-01-01"
end_date <- "2021-12-31"

Expected Results:

under construction

Detailed Instructions

1. Run code

2. Deposit results:

Use this file request link to deposit your entire result_[SITE_NAME] folder.