Five critical care physicians (JMK, COP, BDS, JMW, RGW) retrospectively adjudicated patients as COVID-19 pneumonia, non-COVID-19 viral pneumonia, pneumonia secondary to other pathogens, or non-pneumonia controls (intubated for reasons other than pneumonia), according to a standardized adjudication procedure (the adjudication protocol can be found in Supplemental Data File 8). Non-pneumonia controls were defined as patients who underwent BAL to exclude pneumonia but had negative quantitative cultures, a negative multiplex PCR for viral and bacterial pathogens (when available) and negative urine antigens for Streptococcus pneumoniae and Legionella pneumophilia serogroup 1, as well as an alternative diagnosis. The treating clinician’s impression was considered, but concordance was not required. Subsequent course and the entirety of the clinical record was used for adjudication. Some of the patients adjudicated as non-pneumonia controls developed ventilator-associated pneumonia later in their clinical course. Viral pneumonia was diagnosed based on detection of a respiratory viral pathogen from either a nasopharyngeal swab or BAL fluid in the appropriate clinical setting. Bacterial pneumonia was defined as positive quantitative cultures with > 10^2 colony forming units/ml, detection of a bacterial pathogen by PCR analysis of BAL fluid or a positive urine antigen. Over the course of the study, BAL fluid was analyzed using an MRSA PCR (MRSA/SA SSTI) and the BioFire FilmArray Respiratory 2 (RP2) Panel and Pneumonia panels. SARS-CoV-2 was detected with a variety of assay platforms including the Cepheid Gene Expert, Abbott ID NOW, Becton-Dickinson, and a locally-developed and validated PCR. For some patients without COVID-19, the diagnosis of pneumonia was made based on clinical suspicion, radiographic findings, and response to antimicrobial therapy in the absence of an identified pathogen. Ventilator-associated pneumonia was diagnosed as detection of a new respiratory pathogen using quantitative culture or PCR more than 48 hours after intubation, the detection of a new respiratory pathogen on serial BAL samples, or the reappearance of a respiratory pathogen after a negative BAL on a subsequent study. Clinical laboratory data were obtained from the Northwestern Medicine Enterprise Data Warehouse using Structured Query Language (SQL). APS and SOFA scores were generated from the Electronic Health Record using previously validated programming.

Note: The content above has been extracted from a research article, so it may not display correctly.



Q&A
Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.



We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.