Background: The epidemiology, characteristics and outcomes of coinfections in COVID-19 are still poorly understood.

Methods: We investigated the prevalence of coinfections in COVID-19 patients hospitalized in Switzerland over the first three epidemic waves between 1 March 2020 and 1 June 2021, as well as risk factors and outcomes. Patients were identified from six hospitals of the Swiss prospective surveillance system database (CH-SUR). Details of the type and treatment of coinfections were retrieved retrospectively from medical charts. We assessed the proportion of patients with suspected coinfections and analyzed risk factors and 90-day in-hospital survival using logistic and Cox regression.

Results: Of 13,265 identified patients, 36.6% (4859/13,625) had suspected coinfections, and 44.8% (5941/13,625) received antibiotics. Respiratory coinfections (25.6%) were the most common, followed by bloodstream (19.8%) and urinary tract infections (14.6%). Escherichia coli (14.8%), Staphylococcus aureus (10.7%) and Klebsiella pneumoniae (6.1%) were the most frequently isolated pathogens. The risk factors for coinfections included increasing age, male gender, certain underlying medical conditions and immunosuppression. Suspected coinfections were associated with a longer hospital stay (13 vs. 7 days, p < 0.001), more frequent ICU admission (26% vs. 6.7%, p < 0.001) and higher rates of in-hospital death (24% vs. 9.5%, p < 0.001). Hospitalization in the ICU at the time of COVID-19 diagnosis had the strongest association with coinfections.

Conclusions: A high proportion of COVID-19 patients had coinfections, particularly respiratory infections, and received antibiotics. Coinfections were associated with severe illness and worse outcomes.