Objectives SARS-CoV-2 may cause acute lung injury, and secondary infections are thus relevant complications in patients with COVID-19 pneumonia. However, detailed information on community- and hospital-acquired infections among patients with COVID-19 pneumonia is scarce. Methods We identified 220 SARS-CoV-2-positive patients hospitalized at the University Hospital Basel, Switzerland (between 25 February and 31 May 2020). We excluded patients who declined the general consent (n = 12), patients without clinical evidence of pneumonia (n = 29), and patients hospitalized for < 24 h (n = 17). We evaluated the frequency of community- and hospital-acquired infections using respiratory and blood culture materials with antigen, culture-based, and molecular diagnostics. For ICU patients, all clinical and microbial findings were re-evaluated interdisciplinary (intensive care, infectious disease, and clinical microbiology), and agreement reached to classify patients with infections. Results In the final cohort of 162 hospitalized patients (median age 64.4 years (IQR, 50.4–74.2); 61.1% male), 41 (25.3%) patients were admitted to the intensive care unit, 34/41 (82.9%) required mechanical ventilation, and 17 (10.5%) of all hospitalized patients died. In total, 31 infections were diagnosed including five viral co-infections, 24 bacterial infections, and three fungal infections (ventilator-associated pneumonia, n = 5; tracheobronchitis, n = 13; pneumonia, n = 1; and bloodstream infection, n = 6). Median time to respiratory tract infection was 12.5 days (IQR, 8–18) and time to bloodstream infection 14 days (IQR, 6–30). Hospital-acquired bacterial and fungal infections were more frequent among ICU patients than other patients (36.6% vs. 1.7%). Antibiotic or antifungal treatment was administered in 71 (43.8%) patients. Conclusions Community-acquired viral and bacterial infections were rare among COVID-19 pneumonia patients. By contrast, hospital-acquired bacterial or fungal infections were frequently complicating the course among ICU patients.

Background SARS-CoV-2 emerged in China as the cause of CoVID-19 in December 2019 reaching Europe by late January 2020, when community-acquired respiratory viruses (CARVs) are at their annual peak. We validated the WHO-recommended SARS-CoV-2-assay and analyzed the epidemiology of SARS-CoV-2 and CARVs. Methods Naso-oropharyngeal swabs (NOPS) from 7663 patients were prospectively tested by Basel-S-gene and WHO-based E-gene-assay (Roche) in parallel using Basel-N-gene-assay for confirmation. CARVs were prospectively tested in 2394 NOPS by multiplex-NAT, including 1816 (75%) simultaneously for SARS-CoV-2. Results Basel-S-gene and Roche-E-gene-assays were concordant in 7475 cases (97.5%) including 825 (11%) SARS-CoV-2-positives. In 188 (2.5%) discordant cases, SARS-CoV-2-loads were significantly lower than in concordant positive ones and confirmed in 105 (1.4%). Adults were more frequently SARS-CoV-2-positive, while children tested more frequently CARV-positive. CARV co-infections with SARS-CoV-2 occurred in 1.8%. SARS-CoV-2 replaced CARVs within 3 weeks reaching 48% of all detected respiratory viruses followed by rhino/enterovirus (13%), influenzavirus (12%), coronavirus (9%), respiratory syncytial (6%) and metapneumovirus (6%). Conclusions Winter CARVs were dominant during the early SARS-CoV-2 pandemic impacting infection control and treatment decisions, but were rapidly replaced suggesting competitive infection. We hypothesize that pre-existing immune memory and innate immune interference contribute to the different SARS-CoV-2 epidemiology among adults and children.

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