Bacterial Pneumonia and Respiratory Culture Utilization among Hospitalized Patients with and without COVID-19 in New York City

Abstract

COVID-19 is associated with prolonged hospitalization and a high risk of intubation, which raises concern for bacterial co-infection and antimicrobial resistance. Previous research has shown a wide range of bacterial pneumonia rates for COVID-19 patients in a variety of clinical and demographic settings, but none have compared hospitalized COVID-19 patients to patients testing negative for SARS-CoV-2 in similar care settings. We performed a retrospective cohort study on hospitalized patients with COVID-19 testing from 10 March 2020 to 31 December 2020. A total of 19,219 patients were included, of which 3,796 tested positive for SARS-CoV-2. We found a 2.6-fold increase (p < 0.001) in respiratory culture ordering in COVID-19 patients. On a per-patient basis, COVID-19 patients were 1.5-fold more likely than non-COVID patients to have abnormal respiratory cultures (46.8% vs. 30.9%, p <0.001), which was primarily driven by patients requiring intubation. Among patients with pneumonia, a significantly higher proportion of COVID-19 patients had ventilator-associated pneumonia (VAP) relative to non-COVID patients (85.7% vs 55.1%, p <0.001), but a lower proportion had community-acquired (12.2% vs 22.1%, p < 0.01) or hospital-acquired pneumonia (2.1% vs. 22.8%, p < 0.001). There was also a significantly higher proportion of respiratory cultures positive for MRSA, K. pneumoniae, and antibiotic-resistant organisms in COVID-19 patients. Increased rates of respiratory culture ordering for COVID-19 patients therefore appear to be clinically justified for patients requiring intubation, but further research is needed to understand how SARS-CoV-2 increases the risk of VAP.