Incidence and risk factors for clinically confirmed secondary bacterial infections in patients hospitalized for coronavirus disease 2019 (COVID-19).

OBJECTIVE: The true incidence and risk factors for secondary bacterial infections in coronavirus disease 2019 (COVID-19) remains poorly understood. Knowledge of risk factors for secondary infections in hospitalized patients with COVID-19 is necessary to optimally guide selective use of empiric antimicrobial therapy. DESIGN: Single-center retrospective cohort study of symptomatic inpatients admitted for COVID-19 from April 15, 2020, through June 30, 2021. SETTING: Academic quaternary-care referral center in Portland, Oregon. PATIENTS: The study included patients who were 18 years or older with a positive severe acute respiratory coronavirus virus 2 (SARS-CoV-2) PCR test up to 10 days prior to admission. METHODS: Secondary infections were identified based on clinical, radiographic, and microbiologic data. Logistic regression was used to identify risk factors for secondary infection. We also assessed mortality, length of stay, and empiric antibiotics among those with and without secondary infections. RESULTS: We identified 118 patients for inclusion; 31 (26.3%) had either culture-proven or possible secondary infections among hospitalized patients with COVID-19. Mortality was higher among patients with secondary infections (35.5%) compared to those without secondary infection (4.6%). Empiric antibiotic use on admission was high in both the secondary and no secondary infection groups at 71.0% and 48.3%, respectively. CONCLUSIONS: The incidence of secondary bacterial infection was moderate among hospitalized patients with COVID-19. However, a higher proportion of patients received empiric antibiotics regardless of an identifiable secondary infection. Transfer from an outside hospital, baseline immunosuppressant use, and corticosteroid treatment were independent risk factors for secondary infection. Additional studies are needed to validate risk factors and best guide antimicrobial stewardship efforts.

Understanding viral shedding of severe acute respiratory coronavirus virus 2 (SARS-CoV-2): Review of current literature.

OBJECTIVE: Transmission of SARS-CoV-2 has significant implications for hospital infection prevention and control, discharge management, and public health. We reviewed available literature to reach an evidenced-based consensus on the expected duration of viral shedding. DESIGN: We queried 4 scholarly repositories and search engines for studies reporting SARS-CoV-2 viral shedding dynamics by PCR and/or culture available through September 8, 2020. We calculated the pooled median duration of viral RNA shedding from respiratory and fecal sources. RESULTS: The review included 77 studies on SARS-CoV-2. All studies reported PCR-based testing and 12 also included viral culture data. Among 28 studies, the overall pooled median duration of RNA shedding from respiratory sources was 18.4 days (95% CI, 15.5-21.3; I2 = 98.87%; P < .01). When stratified by disease severity, the pooled median duration of viral RNA shedding from respiratory sources was 19.8 days (95% CI, 16.2-23.5; I2 = 96.42%; P < .01) among severely ill patients and 17.2 days (95% CI, 14.0-20.5; I2 = 95.64%; P < .01) in mild-to-moderate illness. Viral RNA was detected up to 92 days after symptom onset. Viable virus was isolated by culture from -6 to 20 days relative to symptom onset. CONCLUSIONS: SARS-COV-2 RNA shedding can be prolonged, yet high heterogeneity exists. Detection of viral RNA may not correlate with infectivity since available viral culture data suggests shorter durations of shedding of viable virus. Additional data are needed to determine the duration of shedding of viable virus and the implications for risk of transmission.