Antimicrobial Resistance in Patients with COVID-19: A Systematic Review and Meta-Analysis

Background: Frequent use of antibiotics in patients with COVID-19 threatens to fuel the public health threat of antimicrobial resistance (AMR). This study sought to determine the prevalence and predictors of bacterial infections and AMR in patients with COVID-19. Methods: We performed a systematic review of studies evaluating bacterial co-infections (≤48 hours of presentation) and secondary infections (>48 hours after presentation) in outpatients or hospitalised patients with COVID-19. A search strategy using bacterial infection terms was applied to the World Health Organization COVID-19 Research Database on December 1, 2021. Studies reporting on microbiologically-confirmed bacterial infection in any anatomical site were eligible for inclusion. We reported the pooled prevalence of bacterial infections and AMR, by conducting a random-effects meta-analysis. Findings: 148 studies evaluating 362 976 patients were included. The prevalence of bacterial co-infection in COVID-19 patients was 5·3% (95%CI: 3·8–7·4%), whereas prevalence of secondary bacterial infection was 18·4% (95%CI: 14·0 –23·7%). While 93 (63%) studies reported resistance or susceptibility data for at least one species, 42 (28%) reported comprehensive data on the prevalence of AMR. Of patients with documented bacterial infections, 60·8% (95%CI: 38·6 to 79·3%, 17 studies) were infected with resistant pathogens and 37.5% (95%CI: 26·9 to 49·5%, 42 studies) of the organisms were resistant. Significant study-level predictors for AMR included ICU setting, use of IL-6 inhibitors, diabetes, antibiotic use and geographical region (Eastern Mediterranean and Asia). Interpretation: While the prevalence of bacterial co-infections in patients with COVID-19 is low, bacterial secondary infections are more frequent. Although infrequently evaluated, antibiotic resistance is highly prevalent in patients with COVID-19 who develop bacterial infections. These data can help to inform guidelines on appropriate antibiotic use in patients with COVID-19. Future research and surveillance evaluating the impact of COVID-19 on antibiotic resistance at the patient and population level are urgently needed.