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.
