Impact of Pandemic Mitigation Efforts on Colonization and Transmission of Respiratory Pathogens and Antibiotic Resistance Genes

ABSTRACT Nasopharyngeal (NP) colonization with commensal and pathogenic organisms is common and a dynamic process. While these dynamics typically occur in the healthy state, many respiratory viruses and colonizing bacteria are important causes of acute respiratory illness (ARI) and invasive disease. Respiratory viruses and bacteria also exhibit interactions that are important in ARI pathogenesis. The initial period shortly after acquisition of respiratory bacteria or infection with respiratory viruses is particularly critical, imparting an increase in ARI risk. S. pneumoniae, S. aureus, and other colonizing bacteria also commonly express antibiotic resistance genes that may be transferred or exchanged between co-colonizing organisms. Broad mitigation strategies were implemented for SARS-CoV-2 pandemic control in many settings, including use of face coverings, stay-at-home orders, and school closures. Collectively, these efforts were associated with reduced community transmission of SARS-CoV-2. In addition, ecologic studies during these periods also demonstrated interruptions in influenza, respiratory syncytial virus, and S. pneumoniae disease activity that were very substantial, dwarfing the success of existing preventive strategies, including vaccines, which are available against only few respiratory pathogens and limited in their scope and effectiveness. Understanding the impact of mitigation strategies on the activity of colonizing respiratory pathogens beyond SARS-CoV-2 would inform efforts to understand infection dynamics and reduce the burden of these common yet currently unpreventable infections. We conducted intensive household-based ARI surveillance in Lima, Peru during the same period in two consecutive years: 2019, just prior to the COVID-19 pandemic, and 2020, during peak SARS-CoV-2 activity. We aim to leverage this unique platform to characterize patterns of household acquisition and infection with respiratory pathogens during periods with and without mitigation strategies through the conduct of two Specific Aims: 1) To test the hypothesis that mitigation strategies are associated with a) fewer acquisitions of colonizing respiratory bacteria, b) fewer infections with respiratory viruses, shorter durations of colonization/detections, and reduced transmission of these pathogens among children and adults in households in semi-urban Peru, and 2) To test the hypothesis that mitigation strategies are associated with fewer acquisitions, shorter duration of detection, and reduced household transmission of nasopharyngeal antibiotic resistance genes among children and adults in households in semi-urban Peru. A detailed understanding of the impact of these mitigation strategies on the dynamics of colonization with clinically relevant respiratory pathogens may inform targeted applications to reduce the global impact of ARI and pneumonia, particularly for infections that are not yet vaccine-preventable.