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 exacerbate antimicrobial resistance. We aimed to establish the prevalence and predictors of bacterial infections and antimicrobial resistance (AMR) in patients with COVID-19. Methods: We conducted a systematic review and meta-analysis of cohort studies, case series, case-control trials, and randomized controlled trials (≥50 patients) published between Jan 1, 2019, and Dec 1, 2021, from the WHO COVID-19 Research Database. We included outpatients or hospitalized patients with laboratory-confirmed COVID-19 and microbiologically confirmed bacterial co-infections (≤48 h of presentation) or secondary infections (>48 h). Random-effects meta-analysis and meta-regression were used. Primary outcomes were prevalence of bacterial co-infection and secondary infection, and prevalence of antibiotic-resistant pathogens among patients with bacterial infections. PROSPERO: CRD42021297344. Findings: 148 studies (362,976 patients; Dec 2019–May 2021) were included. Pooled prevalence of bacterial co-infection was 5.3% (95% CI 3.8–7.4); secondary bacterial infection 18.4% (14.0–23.7). Among studies comprehensively reporting AMR, 60.8% (38.6–79.3) of bacterial infections were resistant (per-patient), and 37.5% (26.9–49.5) of isolates were resistant (per-organism), with substantial heterogeneity (I² up to 95%). Interpretation: Although infrequently assessed, AMR is highly prevalent among COVID-19 patients with bacterial infections, especially in intensive care unit settings. Enhanced surveillance and judicious antibiotic use are urgently needed. Funding: WHO.