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 in patients with COVID-19. Methods We did a systematic review and meta-analysis of studies of bacterial co-infections (identified within <= 48 h of presentation) and secondary infections (>48 h after presentation) in outpatients or hospitalised patients with COVID-19. We searched the WHO COVID-19 Research Database to identify cohort studies, case series, case-control trials, and randomised controlled trials with populations of at least 50 patients published in any language between Jan 1, 2019, and Dec 1, 2021. Reviews, editorials, letters, pre-prints, and conference proceedings were excluded, as were studies in which bacterial infection was not microbiologically confirmed (or confirmed via nasopharyngeal swab only). We screened titles and abstracts of papers identified by our search, and then assessed the full text of potentially relevant articles. We reported the pooled prevalence of bacterial infections and antimicrobial resistance by doing a randomeffects meta-analysis and meta-regression. Our primary outcomes were the prevalence of bacterial co-infection and secondary infection, and the prevalence of antibiotic-resistant pathogens among patients with laboratory-confirmed COVID-19 and bacterial infections. The study protocol was registered with PROSPERO (CRD42021297344). Findings We included 148 studies of 362 976 patients, which were done between December, 2019, and May, 2021. The prevalence of bacterial co-infection was 5 center dot 3% (95% CI 3 center dot 8-7 center dot 4), whereas the prevalence of secondary bacterial infection was 18 center dot 4% (14 center dot 0-23 center dot 7). 42 (28%) studies included comprehensive data for the prevalence of antimicrobial resistance among bacterial infections. Among people with bacterial infections, the proportion of infections that were resistant to antimicrobials was 60 center dot 8% (95% CI 38 center dot 6-79 center dot 3), and the proportion of isolates that were resistant was 37 center dot 5% (26 center dot 9-49 center dot 5). Heterogeneity in the reported prevalence of antimicrobial resistance in organisms was substantial (I-2=95%). Interpretation Although infrequently assessed, antimicrobial resistance is highly prevalent in patients with COVID-19 and bacterial infections. Future research and surveillance assessing the effect of COVID-19 on antimicrobial resistance at the patient and population level are urgently needed.

Automated summary

Through systematic review and meta-analysis, we found a high prevalence of bacterial infections and antimicrobial resistance in patients with COVID-19. The prevalence of bacterial co-infection in COVID-19 patients was 5.3%, while the prevalence of secondary bacterial infection was 18.4%. Antimicrobial resistance was highly prevalent, with 60.8% of infections and 37.5% of isolates being resistant to antimicrobials.