Understanding respiratory tract infections through minimally-invasive, daily nasal sampling in children

Project Information

DailySAM

Grant agreement ID: 101075118

DOI

10.3030/101075118

EC signature date 6 June 2023

Start date 1 July 2023

End date 30 June 2028

Funded under

• European Research Council (ERC)

Total cost

€ 1 677 858,75

EU contribution

€ 1 677 858,00

Coordinated by

ACADEMISCH ZIEKENHUIS LEIDEN
Netherlands

Periodic Reporting for period 1 - DailySAM (Understanding respiratory tract infections through minimally-invasive, daily nasal sampling in children)

Reporting period: 2023-07-01 to 2025-12-31

Summary of the context and overall objectives of the project

Pneumonia is the number one infectious cause of death in children worldwide. Many of the viruses and bacteria that cause pneumonia are frequently carried in the nose of children without causing disease. This carriage is a driving force for transmission of such pathogens, but is also can boost immunity in these children. However, we still lack understanding of what are the factors that determine how carriage behaves, what drives the formation of immune memory and how transmission works.

We have recently optimized nasal sampling analysis methods using Synthetic Absorptive Matrix (SAM) strips that are tolerated better by children than classical swabs. Because of that it is possible to perform frequent sample collections in children, which is not possible with standard methods like swabs. We will collect samples from children to study naturally-acquired carriage, but also study the nasal live attenuated influenza vaccine in a safe and ethically acceptable manner. In addition, we will perform high frequency nasal sampling in groups of schoolchildren to measure transmission events over time. As there are a large number of bacteria and viruses that can cause disease, we will develop new tools to measure microbes in high-throughput. We will also develop an array to measure antibodies against these bacteria and viruses, measure total microbiome and host responses. We will then perform advanced data analysis to integrate these datasets over time using statistical and mathematical tools to give new insights into key markers related to carriage, transmission and immunity. We will test some of the key findings with in vitro models in which nasal cells are grown and exposed to pathogens in a laboratory environment, which can be used to test associations.

Altogether, the comprehensive and detailed understanding of nasal carriage obtained in this project can lead to better diagnostics, mucosal targeted therapies and vaccines, and provide a basis for the improved predictions of pathogen spread and public health effects of interventions at the population level, such as was seen during the COVID-19 pandemic.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The project isstructured into four work packages (WP1). Below the work performed and main achievements are explained per WP.
WP1 clinical studies.
The study in school children was successfully submitted to the ethical committee (NL85480.058.23). This study has been registered at the Dutch national registry of research with human participants: https://onderzoekmetmensen.nl/en/trial/56507. This study has now been completed. In total, 92 subjects were screened for eligibility, 55 were enrolled in the study, and 54 completed follow-up (98%). From these 55 children and teachers, we collected 1222 samples during routine school visits and 24 samples during illness collected at home.
The live attenuated influenza vaccine study has been submitted to the ethical committee through CTIS, has received ethical approval, and is scheduled to run in the winter of 2025/26

WP2 laboratory measurements.
We developed and validated a novel assay based on qPCR method on a chip to study bacteria and viruses, including 16 viral species, 6 bacterial species, and 21 serotypes of the bacterium S. pneumoniae. This assay was validated against controls with known positivity/negativity, and compared against conventional qPCR. This assay was used to analyse the 1262 samples collected during the first daily sampling study.
We also started the development of an antigen microarray to measure antibodies against the same bacteria and viruses. Antigen and sample preprocessing and concentration conditions were optimized. The assay was validated against validated assays for SARS-CoV-2 spike. However, more work on this is ongoing as some antigens showed crystal formation and require optimization.

WP3 data analysis
We analysed the bacterial/viral carriage dynamics in the first cohort with daily sampling. We were able to find new associations between bacteria in the nose of children, both between bacterial species, but also within bacterial species. We were also able to link bacterial and viral carriage together and identify how presence of some microbes could affect each other. Finally, we could see how viruses and bacteria are linked to symptoms such as snotty noses and coughing in children.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The newly developed microfluidic method for detection of pathogens allows for the screening of a substantial number of respiratory pathogens per sample. This can be applied to a large variety of samples, and the method has been transferred already to several collaborators to be implemented in theirlabs. We expect that publishing this will enable further uptake by the scientific community.

The newly developed array to study antibodies requires further optimization and validation to be able to be implemented.

Our observation of a bacterium that can inhibit viral carriage requires validation in the second cohort and potentially in the live attenuated influenza vaccine study. If this is validated in vivo, work on the mechanisms using in vitro models and immunological analysis is required. Thus further research is needed before this can be developed into a potential intervention.