Introduction Non-pharmaceutical interventions (NPIs), which aimed to reduce transmission of SARS-CoV-2, also reduced the circulation of other respiratory pathogens. However, it remains unclear to what extent NPIs disrupted pneumococcal colonization in childcare settings. We investigated pneumococcal colonization dynamics in childcare centers in the Greater New Haven Area (USA) with varying levels of COVID-19-related NPI recommendations.

Methods Weekly, parent-collected saliva samples were obtained from children attending 8 childcare centers during Spring 2021 (February 2021-June 2021) and Winter/Spring 2021/22 (November 2021-June 2022). Samples were culture-enriched and tested using quantitative polymerase chain (qPCR) for pneumococcus targeting piaB, lytA, and pneumococcal serotypes. Trajectories of pneumococcal colonization were modeled using Markov models adjusted for age, sex, household size, ethnicity and study period. Bayes’ rule was used to adjust for false positivity of detecting non-pneumococcal signals in pneumococcal serotype-specific qPCR assays.

Results A total of 1,100 saliva samples were collected from 100 children aged 0.3-5.9 years (median = 3.3 years, IQR = 1.8-4.6 years). Carriage dynamics based on detection of piaB and lytA were largely similar. Aggregated piaB-based carriage prevalence was higher during Winter/Spring 2021/22 (52.8%, 95% Confidence Interval: 49.4-56.3) than Spring 2021 (30.7%, 25.4-36.5). This increase in prevalence during Winter/Spring 2021/22 was driven by a higher proportion of high-density carriers, coinciding with less stringent NPI measures.

Overall carriage acquisition rates were also higher during Winter/Spring 2021/22 than Spring 2021 (Hazard Ratio [HR]: 2.88, 1.09-7.60). The most commonly prevalent serotypes were 15B/C, 11A/D/E and 33F/A/37.

Conclusions We observed distinct patterns of pneumococcal carriage between Spring 2021 and Winter/Spring 2021/22 of the COVID-19 pandemic, among children attending New Haven childcare centers. The increase in carriage prevalence coincided with the relaxation of COVID-19 NPI measures during Winter/Spring 2021/22 and an increase in local cases of certain respiratory viruses.

DMW has received consulting fees from Pfizer, Merck, and GSK and is PI on research grants from Pfizer and Merck. ALW is currently an employee of Pfizer, Inc. ALW has previously received consulting and/or advisory board fees from Pfizer, Merck, Diasorin, PPS Health, Co-Diagnostics, and Global Diagnostic Systems for work unrelated to this project. All other co-authors declare no potential conflict of interest

The study was supported by Merck Investigators Studies Program to ALW. This work was also supported, in part, from grants by the National Institutes of Health grant numbers K23AI159518 to CO. The study protocol was designed by the Yale researchers. The funder had no role in study design, data collection, data analysis, data interpretation, or writing of the report. The decision to publish was made by the Yale researchers; all authors agree with the decision to publish and with the results of the study

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The study was approved by the Institutional Review Board of the Yale Human Research Protection Program (Protocol number: 200002839). Parents or guardians provided written informed consent for their children to participate in the study.

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