ABSTRACT
COVID-19 pandemic responses have dramatically modified the global ecological and epidemiological landscape of many infectious diseases. However, the pandemics impacts on antimicrobial resistance (AMR) are currently poorly understood and lack data. While surges in COVID-19 cases during the first wave of the pandemic may have exacerbated AMR, decreases in antibiotic use may have had the opposite effect. To disentangle how pandemic impacts such as lockdowns and modified antibiotic prescribing may affect AMR, we developed a mathematical model formalizing simultaneous transmission of SARS-CoV-2 and colonization with a bacterial pathogen across six pandemic scenarios. We used simulation to assess the effect of each scenario on the bacterial carriage prevalence, antibiotic resistance rate, and the invasive bacterial disease (IBD) incidence, using parameters based on the commensal community bacterium Streptococcus pneumoniae. Pandemic scenarios without community-wide lockdowns all resulted in a decrease in carriage prevalence of antibiotic-sensitive bacteria and an increase in the prevalence of antibiotic-resistant bacteria, while the addition of a population-wide lockdown resulted in a large reduction in colonization prevalence and IBD incidence for both strains (>70%). This translated to an increase in the antibiotic resistance rate across all scenarios to varying degrees, with lingering effects after the cessation of COVID-19 response measures. In the absence of lockdown, a population-wide surge in antibiotic prescribing coincident with the peak in SARS-CoV-2 infection resulted in the greatest increases in resistance rate (23%) and resistant IBD incidence (6%). Within-host interactions, SARS-CoV-2 variants, and population immunity are found to further drive the magnitude of pandemic impacts on resistant IBD incidence. Sensitivity analyses suggest that the extent of such impacts likely varies across different bacterial species. Although real-life scenarios are significantly more complicated, our findings suggest that COVID-19 pandemic responses may significantly impact antibiotic resistance in the community and support the need for monitoring resistance during pandemic waves. Author SummaryAntimicrobial resistance (AMR) is a leading threat to global health. The ongoing COVID-19 pandemic has occurred during global efforts to combat AMR, and pandemic responses implemented to slow SARS-CoV-2 transmission have dramatically affected the incidence of common viral and bacterial respiratory infections at a global scale. However, impacts of the COVID-19 pandemic on AMR and the incidence of invasive bacterial disease (IBD) caused by antibiotic-resistant bacteria are still being uncovered. Here, we use mathematical modelling to explore how different pandemic scenarios accounting for variation in lockdown implementation and antibiotic use in the community may affect antibiotic-resistant bacteria. We found that lockdown implementation substantially reduces the number of annual cases of resistant IBD (over 70%), although the proportion of resistant bacteria among carriers is expected to increase when prophylactic antibiotics are prescribed in response to SARS-CoV-2 infection. We also found that a population-wide surge in antibiotic prescribing in the absence of lockdown may contribute to a large increase (6%) in the number of IBD cases caused by antibiotic-resistant bacteria, while the effect of reduced antibiotic use is negligible. However, such impacts likely vary depending on the bacterial species considered, within-host interactions, SARS-CoV-2 variants, and population immunization levels.