Cleary, David W., Campling, James, Lahuerta, Maria, Hayford, Kyla, Southern, Jo, Gessner, Bradford D., Lo, Stephanie W., Bentley, Stephen D., Faust, Saul N. and Clarke, Stuart C. (2024) Non-pharmaceutical interventions for COVID-19 transiently reduced pneumococcal and Haemophilus influenzae carriage in a cross-sectional paediatric cohort in Southampton, UK. Microbiology Spectrum.
Abstract
The Southampton pneumococcal carriage study of children under five years old continued during the COVID-19 pandemic. Here, we present data from October 2018 to March 2023 describing prevalence of pneumococci and other pathobionts during the winter seasons before, during and after the introduction of non-pharmaceutical interventions (NPIs) to prevent SARS-CoV-2 transmission. Nasopharyngeal swabs were collected from children attending outpatient clinics at a secondary care hospital and community health-care sites. Pre-NPIs, in 2019/20, the carriage prevalence of pneumococci at the hospital site was 32% (n=161 positive/499 participants). During NPIs, this fell to 19% (n=12/64), although based on fewer participants compared to previous years due to COVID-19 restrictions on health-care attendance. In 2021/22, after NPIs had eased, prevalence rebounded to 33% (n=15/46) (compared to NPIs period, X2 (1, N=110) = 2.78, p=0.09)). Carriage prevalence at community health-care sites fell significantly from 27% (n=127/470) in 2019/20 to 19% during the NPIs period (n=44/228) in 2020/21 (X2 (1, N=698) = 4.95, p=0.026)). No rebound was observed in 2021/22 (19% (n=56/288). However, in a multivariate logistic regression model, neither site had a significantly lower carriage prevalence during the NPIs period compared to the post NPIs period. A reduction in serotype diversity was observed 2020/21. Carriage of Haemophilus influenzae was particularly affected by NPIs with a significant reduction observed. In conclusion, among children under 5 years of age, transient, modest, and statistically non-significant alterations in carriage of both S. pneumoniae and H. influenzae were associated with SARS-CoV2 NPIs.
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