AUTHOR=Bennett Julia C. , Emanuels Anne , Heimonen Jessica , O'Hanlon Jessica , Hughes James P. , Han Peter D. , Chow Eric J. , Ogokeh Constance E. , Rolfes Melissa A. , Lockwood Christine M. , Pfau Brian , Uyeki Timothy M. , Shendure Jay , Hoag Samara , Fay Kairsten , Lee Jover , Sibley Thomas R. , Rogers Julia H. , Starita Lea M. , Englund Janet A. , Chu Helen Y. 

TITLE=Streptococcus pneumoniae nasal carriage patterns with and without common respiratory virus detections in households in Seattle, WA, USA before and during the COVID-19 pandemic

JOURNAL=Frontiers in Pediatrics

VOLUME=11

YEAR=2023

URL=https://www.frontiersin.org/journals/pediatrics/articles/10.3389/fped.2023.1198278

DOI=10.3389/fped.2023.1198278

ISSN=2296-2360

ABSTRACT=<sec><title>Background</title><p>Respiratory viruses might influence <italic>Streptococcus pneumoniae</italic> nasal carriage and subsequent disease risk. We estimated the association between common respiratory viruses and semiquantitative <italic>S. pneumoniae</italic> nasal carriage density in a household setting before and during the COVID-19 pandemic.</p></sec><sec><title>Methods</title><p>From November 2019–June 2021, we enrolled participants in a remote household surveillance study of respiratory pathogens. Participants submitted weekly reports of acute respiratory illness (ARI) symptoms. Mid-turbinate or anterior nasal swabs were self-collected at enrollment, when ARI occurred, and, in the second year of the study only, from household contacts after SARS-CoV-2 was detected in a household member. Specimens were tested using multiplex reverse-transcription PCR for respiratory pathogens, including <italic>S. pneumoniae</italic>, rhinovirus, adenovirus, common human coronavirus, influenza A/B virus, respiratory syncytial virus (RSV) A/B, human metapneumovirus, enterovirus, and human parainfluenza virus. We estimated differences in semiquantitative <italic>S. pneumoniae</italic> nasal carriage density, estimated by the inverse of <italic>S. pneumoniae</italic> relative cycle threshold (Crt) values, with and without viral detection for any virus and for specific respiratory viruses using linear generalized estimating equations of <italic>S. pneumoniae</italic> Crt values on virus detection adjusted for age and swab type and accounting for clustering of swabs within households.</p></sec><sec><title>Results</title><p>We collected 346 swabs from 239 individuals in 151 households that tested positive for <italic>S. pneumoniae</italic> (<italic>n</italic> = 157 with and 189 without ≥1 viruses co-detected). Difficulty breathing, cough, and runny nose were more commonly reported among individuals with specimens with viral co-detection compared to without (15%, 80% and 93% vs. 8%, 57%, and 51%, respectively) and ear pain and headache were less commonly reported (3% and 26% vs. 16% and 41%, respectively). For specific viruses among all ages, semiquantitative <italic>S. pneumoniae</italic> nasal carriage density was greater with viral co-detection for enterovirus, RSV A/B, adenovirus, rhinovirus, and common human coronavirus (<italic>P</italic> &lt; 0.01 for each). When stratified by age, semiquantitative <italic>S. pneumoniae</italic> nasal carriage density was significantly greater with viral co-detection among children aged &lt;5 (<italic>P</italic> = 0.002) and 5–17 years (<italic>P</italic> = 0.005), but not among adults aged 18–64 years (<italic>P</italic> = 0.29).</p></sec><sec><title>Conclusion</title><p>Detection of common respiratory viruses was associated with greater concurrent <italic>S. pneumoniae</italic> semiquantitative nasal carriage density in a household setting among children, but not adults.</p></sec>