Multi-year, winter-specific wastewater surveillance during and after the COVID-19 pandemic reveals temporal changes in antibiotic resistance genes, mobile genetic elements, and bacterial communities

Evidence suggests that antimicrobial resistant organisms were able to proliferate during and after the COVID-19 pandemic due to antibiotic misuse, attempts to find appropriate COVID-19 treatment, and secondary infection treatment. Wastewater surveillance has allowed for community-wide data collection and resistance gene trend identification. However, possible long-term impacts of the COVID-19 pandemic on antibiotic resistance in the years following 2020 have not been fully investigated. Weekly wastewater influent samples collected over four months each year from 2021 to 2024 were grouped by year and compared 2021–2022 (higher median SARS-CoV-2 detection) to evaluate the pandemic's impact on antibiotic resistance and microbial communities. The analysis revealed multiple ARGs and MGEs of risk to human health that increased in both relative and absolute abundance (147.3% and 661.4%, respectively) from 2021-2022 to 2023–2024, alongside notable year-to-year shifts in bacterial profiles. Conversely, one ARG, erm F, recorded a higher relative abundance during higher SARS-CoV-2 detection periods compared to the subsequent years with lower SARS-CoV-2 detection. Our research reveals a trend of increased abundance for multiple ARGs/MGEs as well as significant changes to the wastewater bacterial community post-2021-2022, corresponding to significant changes to healthcare and sanitation practices at the time.