Bacterial and Viral Coinfections in Adult Patients Hospitalized With COVID-19 Throughout the Pandemic: A Multinational Cohort Study in the EuCARE Project

Abstract

Background: Limited evidence exists on how bacterial and viral coinfections have developed since the SARS-CoV-2 Omicron variant emerged. We investigated whether community-onset coinfections in adult patients hospitalized with COVID-19 differed during the wild type, Alpha, Delta, and Omicron periods and whether such coinfections were associated with an increased risk of mortality.

Methods: We conducted a multinational cohort study including COVID-19 hospitalizations until 30 April 2023 in 5 European countries. The outcome was bacterial and viral coinfections based on 5 test modalities. Variant periods were compared with regard to occurrences of coinfections and risk ratios for coinfections (Omicron vs pre-Omicron), as well as association with in-hospital mortality (Omicron vs pre-Omicron).

Results: A total of 29 564 cases were included: 12 601 wild type, 5256 Alpha, 2433 Delta, and 9274 Omicron. The coinfection rate was 2.6% (327/12 601) for wild type, 2.0% (105/5256) for Alpha, 3.2% (77/2433) for Delta, and 7.9% (737/9274) for Omicron. Omicron had a significantly increased risk ratio of coinfection when compared with preceding variants (1.88 [95% CI, 1.53-2.32], P < .001). These results were consistent across several subgroup analyses. An increased occurrence (19% [232/1246] vs 11% [3042/28 318]) and adjusted risk (1.69 [95% CI, 1.49-1.91], P < .001) of in-hospital mortality were observed in patients with a verified coinfection as compared with patients without a coinfection.

Conclusions: Bacterial and viral coinfections were more prevalent during the Omicron period as compared with preceding variants. Such coinfections were associated with an increased risk of in-hospital mortality, calling for sustained monitoring and clinical vigilance.

Keywords: COVID-19; SARS-CoV-2; antimicrobial stewardship; coinfection; mortality.