Electronic health record

We used data reporting functions available through the electronic health record (Epic Systems, Verona, WI, USA) shared by all Mass General Brigham health care system institutions. We collected data on all patients 18 years or older who tested positive for COVID-19 during an inpatient, outpatient, or emergency room visit between February 1, 2020, and April 14, 2020. We revisited the records on April 25, 2020, to collect follow-up data on mortality and other outcomes.
Patients who presented to Mass General Brigham institutions with symptoms of fever, cough, sore throat, fatigue, muscle aches, or new anosmia; who were exposed to someone who tested positive for COVID-19; or who were referred by a health care provider were tested per specified testing criteria/guidelines set forth by the institution. Patients were diagnosed as infected with COVID-19 if SARS-CoV-2 RNA was detected in upper or lower respiratory specimens by nucleic acid testing (NAT) assays designated for emergency use authorization (EUA) by the Food and Drug Administration (FDA) and in accordance with the Centers for Disease Control and Prevention (CDC) guidelines [20 , 21 ]. Each assay targets at least 1 SARS-CoV-2 gene region; positive results are reported for each assay, as defined by the manufacturer or reference laboratory.

We used the electronic health record (Epic Systems, Verona, WI), which contains information on inpatient and outpatient visits, to extract data on demographics, comorbidities, smoking, vital signs, comorbidities, laboratory values, and use of extracorporeal oxygenation, high flow oxygen, and mechanical ventilation. All data in the electronic health record were used to extract information, including problem lists, medical history section, or encounter diagnoses from previous inpatient and outpatient visits.

Study data were obtained from the electronic health record (Epic Systems, Verona, WI), which is an integrated electronic health record including all inpatient and outpatient visits in the health system. For data on tobacco use, body mass index (BMI), and comorbidities, we included any data in the electronic health record, including data entered during previous inpatient or outpatient visits in the problem list, medical history section, or on encounter diagnoses.

Since 2003 we have used Epic Systems’ Electronic Health Record across the full range of inpatient and outpatient care. Part of this exclusively electronic documentation is a locally developed, comprehensive Enterprise Data Warehouse with searchable content, including all physiological data, laboratory results, orders, medication prescriptions, administration events, laboratory and pathology data, and the full text of provider notes. We used NorthShore’s Enterprise Data Warehouse to obtain data regarding each patient’s characteristics as well as the results of active surveillance testing for MRSA and any decolonization therapy during the inpatient stay [18 (link)]. The majority of isolates were from unique patients, but because we were investigating the development of resistance over time some patients contributed >1 isolate. No more than 1 unique isolate was included per patient per month. In the analysis, we used time-series modeling (ie, error terms being correlated by an autoregressive process) to account for this approach.