ABSTRACT 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 colonisation in childcare settings. We investigated pneumococcal colonisation dynamics in childcare centers in the Greater New Haven Area (USA) with varying levels of COVID-19-related NPI recommendations.
Methods We collected longitudinal saliva samples from 100 children attending childcare centers during Spring 2021 (February 2021-June 2021) and Winter/Spring 2021/22 (November 2021-June 2022). Weekly parent-collected samples were culture-enriched and tested using quantitative polymerase chain reaction (qPCR) for pneumococcus targeting piaB, lytA, and pneumococcal-specific serotypes. Trajectories of pneumococcal colonisation 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 serotypes in saliva samples.
Results A total of 1,100 saliva samples were collected in 8 childcare centers from 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 observed 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) as stringency levels of NPI lessened, and this difference was seen among high-density carriers. Overall carriage acquisition rates were higher during Winter/Spring 2021/22 than Spring 2021 (Hazard Ratio [HR]: 2.88, 1.09-7.60). The most commonly prevalent serogroups in this population were 15B/C, 11A/D/E and 33F/A/37.
Conclusions We found distinct patterns of carriage between Spring 2021 and Winter/Spring 2021/22 of the COVID-19 pandemic, in the presence of high carriage prevalence among childcare children. Changes in carriage patterns coincided with relaxation of COVID-19 NPI measures during Winter/Spring 2021/22.