High-resolution characterization of nasal microbial dynamics in young children

Dennis Hoving, Rosanne A.M. Steenbergen, Youvika Singh, Dima El Safadi, Ester L. German, Ivana Barros de Campos, Elandri Fourie, Mara van Roermund, Alicia C. de Kroon, Iris van der Valk, Debby Bogaert, Els Wessels, Jutte J.C. de Vries, Willem R. Miellet, Krzysztof Trzciński, Daniela M. Ferreira, Marlies A. van Houten, Simon P. Jochems
2025 · doi:10.1101/2025.08.22.25334231
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Abstract

Nasal carriage of bacteria and viruses is common in young children. However, these carriage dynamics remain poorly understood due to the lack of high-resolution studies. Therefore, we conducted a 29-day prospective study in which 45 children, 1-5 years of age, provided daily nasosorption samples from which we analyzed 16 viruses, 6 bacteria, and 21 Streptococcus pneumoniae serotypes/groups. Bacterial densities fluctuated rapidly, with autocorrelations lasting only eight days. Inter-species but also intra-species interactions were observed; co-carriage of multiple Streptococcus pneumoniae serotypes increased clearance of non-dominant strains. Staphylococcus aureus carriage was associated with reduced viral acquisition and accelerated viral clearance. Rhinovirus triggered rhinitis on the day of acquisition, with bacterial densities rising three days later. This high-resolution sampling approach elucidated complex microbial and host-pathogen interactions in children.
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Abstract Nasal carriage of bacteria and viruses is common in young children. However, these carriage dynamics remain poorly understood due to the lack of high-resolution studies. Therefore, we conducted a 29-day prospective study in which 45 children, 1-5 years of age, provided daily nasosorption samples from which we analyzed 16 viruses, 6 bacteria, and 21 Streptococcus pneumoniae serotypes/groups. Bacterial densities fluctuated rapidly, with autocorrelations lasting only eight days. Inter-species but also intra-species interactions were observed; co-carriage of multiple Streptococcus pneumoniae serotypes increased clearance of non-dominant strains. Staphylococcus aureus carriage was associated with reduced viral acquisition and accelerated viral clearance. Rhinovirus triggered rhinitis on the day of acquisition, with bacterial densities rising three days later. This high-resolution sampling approach elucidated complex microbial and host-pathogen interactions in children. Competing Interest Statement The authors have declared no competing interest. Funding Statement Funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. This work is supported by an ERC grant (DailySAM, 101075118) and the Gates Foundation (INV-008088) to SPJ. IBC had a fellowship from the São Paulo Research Foundation (FAPESP), Brazil (Process Number #2023/14279-9). Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Medical Ethics Committee Leiden The Hague Delft of the Leiden University Medical Centre gave ethical approval for this work I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Footnotes ↵* Joint senior authors Influenza A results from Biomark were confirmed with single-assay conventional PCR. Data Availability All data produced in the present study are available upon reasonable request to the authors Data availability Data can be requested from the corresponding author. An MTA will be required to ensure compliance with ethically approved protocol and privacy regulations prior to transfer of data.

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